I am getting completely different results when I conduct PCA on PLINK and on HAIL - does anyone know why? When I say the results …

I downloaded the following vcf file from https://www.internationalgenome.org/. http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz I wanted to first try and calculate allele frequencies, and then from there calculate allele frequencies …

I'm using plink 1.9 and running the command: plink --bfile data --genome --extract data.prune.in --remove data.fail_imiss where data.fail_imiss is a file with individuals with proportions …

I recently used PLINK to remove missingness in my SNPs data. I always saw message from terminal Web-based version check ( --noweb to skip ) …

I was reading on the metaspades manual that metaspades only works with a single short-read library which has to be paired-end. what does this exactly …

Is it possible to do a PLINK (1.9) meta-analysis using .qassoc files as input? The files look like: CHR SNP BP NMISS BETA SE R2 …

Hi guys, I'm trying to use PLINK to perform a 2-degree-of-freedom test to jointly test the main genetic effect as well as the interaction effect …

Hi, I was running plink(1.9) tool to create bed file (`plink --file inputfile --make-bed --noweb --out outputfile`) which worked fine, but when I switched to …

When I do the imputation using mimimac2, the results showed like below: ``` #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 1_201312170-01 2_201312504-01 6_201313899-01 …

Hello, I am trying to convert a .bam file to a .pileup using samtools and filtering the sites via a .bed file I obtained from …